Locus 8268

Sequence ID	3L_DroMel_CAF1
Location	21,721,934 – 21,722,078
Length	144
Max. P	0.781318

overview

Window 9

Location	21,721,934 – 21,722,038
Length	104
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	89.83
Mean single sequence MFE	-34.48
Consensus MFE	-27.35
Energy contribution	-28.60
Covariance contribution	1.25
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.79
SVM decision value	0.56
SVM RNA-class probability	0.781318
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21721934 104 - 23771897
UCGAUGUCGGGGUCGCUCGAACAUCGAGCAUUGAGCAU-------CGAGCAUUGGGCAUUGUCAGCAGUCCCGUUCAACAAAGGGACAAUGUUUCUCGAUAAAUAUUGUUG
(((((((((((....)))).)))))))..((((((...-------.((((((((((.((((....)))))))((((.......)))))))))))))))))........... ( -32.50)
>DroSec_CAF1 3882 111 - 1
UCGAUGUCGGGGUCGCUCGAACAUCGAGCAUUGAGCAUCGAGCAUCGAGCAUUGGGCAUUGUCAGCAGUCCCGUUCAACAAAGGGACAAUGUUUCUCGAUAAAUAUUGUUG
.(((((((.((...((((((...((((((.....)).))))...)))))).)).))))))).((((.(((((..........)))))(((((((......))))))))))) ( -37.50)
>DroSim_CAF1 8571 111 - 1
UCGAUGUCGGGGUCGCUCGAACAUCGAGCAUUGAGCAUCGAGCAUCGAGCAUUGGGCAUUGUCAGCAGUCCCGUUCAACAAAGGGACAAUGUUUCUCGAUAAAUAUUGUUG
.(((((((.((...((((((...((((((.....)).))))...)))))).)).))))))).((((.(((((..........)))))(((((((......))))))))))) ( -37.50)
>DroYak_CAF1 54452 97 - 1
UCGAUGUCGGGGUCGUUCGAACAUCGAACAUUGGGCA--------------UUGAGCAUUGUCAGCAGUGCCGUGCAACAAAGGGACAAUGUUUCUCGAUAAAUAUUGUUG
((((((((.((...(((((.....))))).)).))))--------------))))((((((....)))))).............((((((((((......)))))))))). ( -30.40)
>consensus
UCGAUGUCGGGGUCGCUCGAACAUCGAGCAUUGAGCAU_______CGAGCAUUGGGCAUUGUCAGCAGUCCCGUUCAACAAAGGGACAAUGUUUCUCGAUAAAUAUUGUUG
(((((((((((....)))).)))))))...((((((.(((.....))).....(((.((((....)))))))))))))......((((((((((......)))))))))). (-27.35 = -28.60 +   1.25)

alignment

secondary structure

dotplot

Window 0

Location	21,721,974 – 21,722,078
Length	104
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	90.29
Mean single sequence MFE	-39.05
Consensus MFE	-32.92
Energy contribution	-32.36
Covariance contribution	-0.56
Combinations/Pair	1.07
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	0.36
SVM RNA-class probability	0.704755
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21721974 104 + 23771897
GGACUGCUGACAAUGCCCAAUGCUCG-------AUGCUCAAUGCUCGAUGUUCGAGCGACCCCGACAUCGAGGGUUGACUGUGCGGUAUGUCAUCGCUUGGCAGGGAAACA
...((((..(.......((((.((((-------(((.((..((((((.....)))))).....))))))))).)))).....(((((.....))))))..))))(....). ( -38.40)
>DroSec_CAF1 3922 111 + 1
GGACUGCUGACAAUGCCCAAUGCUCGAUGCUCGAUGCUCAAUGCUCGAUGUUCGAGCGACCCCGACAUCGAGGGUUGACUGUGCGGUAUGUCAUCGCUUGGCAGGGAAACA
...(((((((((.((((((..((((((.((((((.((.....)))))).))))))))(((((((....)).))))).....)).)))))))).......)))))(....). ( -42.51)
>DroSim_CAF1 8611 111 + 1
GGACUGCUGACAAUGCCCAAUGCUCGAUGCUCGAUGCUCAAUGCUCGAUGUUCGAGCGACCCCGACAUCGAGGGUUGACUGUGCGGUAUGUCAUCGCUUGGCAGGGAAACA
...(((((((((.((((((..((((((.((((((.((.....)))))).))))))))(((((((....)).))))).....)).)))))))).......)))))(....). ( -42.51)
>DroYak_CAF1 54492 97 + 1
GCACUGCUGACAAUGCUCAA--------------UGCCCAAUGUUCGAUGUUCGAACGACCCCGACAUCGAGGGUUGACUGUGCGGUAUGUCAUCGCUUGGCAGGGAAACA
...((((..((.(((....(--------------((((((..(((((.....)))))(((((((....)).))))).....)).)))))..))).).)..))))(....). ( -32.80)
>consensus
GGACUGCUGACAAUGCCCAAUGCUCG_______AUGCUCAAUGCUCGAUGUUCGAGCGACCCCGACAUCGAGGGUUGACUGUGCGGUAUGUCAUCGCUUGGCAGGGAAACA
...(((((((((.((((((.......................(((((.....)))))(((((((....)).))))).....)).)))))))).......)))))(....). (-32.92 = -32.36 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:57 2006